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Thread: New DNA Papers

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    New DNA Papers

    As the title states - This was a thread I greatly enjoyed creating and adding to in DNA-Forums. Click the titles to access the abstracts on PubMed. Links to full papers and supplementaries included where possible.

    Genetic analysis of Y chromosome and mitochondrial DNA poly-morphism of Mulam ethnic group in Guangxi, China
    Wang XQ, Wang CC, Deng QY, Li H.
     
    In order to study the molecular genetic structure of Mulam ethnic group in Guangxi, China, Y chromosome and mitochondrial DNA(mtDNA)polymorphisms were genotyped. High frequencies of the Y chromosome haplogroups O1a1-P203 and O2a1*-M95 were found in Mulam, exhibiting a pattern similar to the neighboring indigenous populations, especially the Daic populations. MtDNA lineages F1a, M*, B4a, B5a, M7b, and N9a were found in Mulam, which always present at high frequencies among the populations of East Asia. Mulam exhibits genetic characteristics of southern Chinese in both paternal and maternal lineages. Multiplex detection of the 17 Y-STR loci and mtDNA HVS-I revealed the distribu-tion of highly genetic diversity in Mulam, which would have potential application in population genetics and forensic practice.

    Introducing the algerian mitochondrial DNA and y-chromosome profiles into the north african landscape.
    Bekada A, Fregel R, Cabrera VM, Larruga JM, Pestano J, Benhamamouch S, González AM. [FULL PAPER]
     
    North Africa is considered a distinct geographic and ethnic entity within Africa. Although modern humans originated in this Continent, studies of mitochondrial DNA (mtDNA) and Y-chromosome genealogical markers provide evidence that the North African gene pool has been shaped by the back-migration of several Eurasian lineages in Paleolithic and Neolithic times. More recent influences from sub-Saharan Africa and Mediterranean Europe are also evident. The presence of East-West and North-South haplogroup frequency gradients strongly reinforces the genetic complexity of this region. However, this genetic scenario is beset with a notable gap, which is the lack of consistent information for Algeria, the largest country in the Maghreb. To fill this gap, we analyzed a sample of 240 unrelated subjects from a northwest Algeria cosmopolitan population using mtDNA sequences and Y-chromosome biallelic polymorphisms, focusing on the fine dissection of haplogroups E and R, which are the most prevalent in North Africa and Europe respectively. The Eurasian component in Algeria reached 80% for mtDNA and 90% for Y-chromosome. However, within them, the North African genetic component for mtDNA (U6 and M1; 20%) is significantly smaller than the paternal (E-M81 and E-V65; 70%). The unexpected presence of the European-derived Y-chromosome lineages R-M412, R-S116, R-U152 and R-M529 in Algeria and the rest of the Maghreb could be the counterparts of the mtDNA H1, H3 and V subgroups, pointing to direct maritime contacts between the European and North African sides of the western Mediterranean. Female influx of sub-Saharan Africans into Algeria (20%) is also significantly greater than the male (10%). In spite of these sexual asymmetries, the Algerian uniparental profiles faithfully correlate between each other and with the geography.

    Assignment of Y-chromosomal SNPs found in Japanese population to Y-chromosomal haplogroup tree.
    Naitoh S, Kasahara-Nonaka I, Minaguchi K, Nambiar P.
     

    The relationship between Y-chromosome single-nucleotide polymorphisms (SNPs) registered in the Japanese SNP (JSNP) database (http://snp.ims.u-tokyo.ac.jp) and Y-binary haplogroup lineages was investigated to identify new Y-chromosomal binary haplogroup markers and further refine Y-chromosomal haplogroup classification in the Japanese population. We used SNPs for which it was possible to construct primers to make Y-specific PCR product sizes small enough to obtain amplification products even from degraded DNA, as this would allow their use not only in genetic but also in archeological and forensic studies. The genotype of 35 JSNP markers were determined, of which 14 were assigned to appropriate positions on the Y-chromosomal haplogroup tree, together with 5 additional new non-JSNP markers. These markers defined 14 new branches (C3/64562+13, C3/2613-27, D2a1b/006841*, D2a1b/119166-11A, D2a/022456*, D2a/119166-11A, D2a/119167rec/119167-40rec*, D2a/75888-GC, O3a3c/075888-9T/10T*, O3a3c/075888-9T/9T, O3a3/8425+6, O3a3/119166-13A*, O3a3/008002 and O3a4/037852) and 21 new internal markers on the 2008 Y-chromosome haplogroup tree. These results will provide useful information for Y-chromosomal polymorphic studies of East Asian populations, particularly those in and around Japan, in the fields of anthropology, genetics and forensics.

    Mitochondrial and Y-chromosomal profile of the Kazakh population from East Kazakhstan.
    Tarlykov PV, Zholdybayeva EV, Akilzhanova AR, Nurkina ZM, Sabitov ZM, Rakhypbekov TK, Ramanculov EM. [FULL PAPER]
     
    Aim. To study the genetic relationship of Kazakhs from East Kazakhstan to other Eurasian populations by examining paternal and maternal DNA lineages. Methods. Whole blood samples were collected in 2010 from 160 unrelated healthy Kazakhs residing in East Kazakhstan. Genomic DNA was extracted with Wizard® genomic DNA Purification Kit. Nucleotide sequence of hypervariable segment I of mitochondrial DNA (mtDNA) was determined and analyzed. Seventeen Y-short tandem repeat (STR) loci were studied in 67 samples with the AmpFiSTR Y-filer PCR Amplification Kit. In addition, mtDNA data for 2701 individuals and Y-STR data for 677 individuals were retrieved from the literature for comparison. Results. There was a high degree of genetic differentiation on the level of mitochondrial DNA. The majority of maternal lineages belonged to haplogroups common in Central Asia. In contrast, Y-STR data showed very low genetic diversity, with the relative frequency of the predominant haplotype of 0.612. Conclusion. The results revealed different migration patterns in the population sample, showing there had been more migration among women. mtDNA genetic diversity in this population was equivalent to that in other Central Asian populations. Genetic evidence suggests the existence of a single paternal founder lineage in the population of East Kazakhstan, which is consistent with verbal genealogical data of the local tribes.

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    MtDNA control region variation affirms diversity and deep sub-structure in populations from Southern Africa.
    Schlebusch CM, Lombard M, Soodyall H.
     

    BACKGROUND:
    The current San and Khoe populations are remnant groups of a much larger and widely dispersed population of hunter-gatherers and pastoralists, who had exclusive occupation of southern Africa before the influx of Bantu-speakers from 2 ka (ka = kilo annum [thousand years] old/ago) and sea-borne immigrants within the last 350 years. Here we use mitochondrial DNA (mtDNA) to examine the population structure of various San and Khoe groups, including seven different Khoe-San groups (Ju/'hoansi, !Xun, /Gui+//Gana, Khwe, =Khomani, Nama and Karretjie People), three different Coloured groups and seven other comparative groups. MtDNA hyper variable segments I and II (HVS I and HVS II) together with selected mtDNA coding region SNPs were used to assign 538 individuals to 18 haplogroups encompassing 245 unique haplotypes. Data were further analyzed to assess haplogroup histories and the genetic affinities of the various San, Khoe and Coloured populations. Where possible, we tentatively contextualize the genetic trends through time against key trends known from the archaeological record.
    RESULTS:
    The most striking observation from this study was the high frequencies of the oldest mtDNA haplogroups (L0d and L0k) that can be traced back in time to ~100 ka, found at high frequencies in Khoe-San and sampled Coloured groups. Furthermore, the L0d/k sub-haplogroups were differentially distributed in the different Khoe-San and Coloured groups and had different signals of expansion, which suggested different associated demographic histories. When populations were compared to each other, San groups from the northern parts of southern Africa (Ju speaking: !Xun, Ju/'hoansi and Khoe-speaking: /Gui+//Gana) grouped together and southern groups (historically Tuu speaking: =Khomani and Karretjie People and some Coloured groups) grouped together. The Khoe group (Nama) clustered with the southern Khoe-San and Coloured groups. The Khwe mtDNA profile was very different from other Khoe-San groups with high proportions of Bantu-speaking admixture but also unique distributions of other mtDNA lineages.
    CONCLUSIONS:
    On the whole, the research reported here presented new insights into the multifaceted demographic history that shaped the existing genetic landscape of the Khoe-San and Coloured populations of southern Africa.

    Genetic data suggests that the Jinggouzi people are associated with the Donghu, an ancient nomadic group of North China.
    Wang H, Chen L, Ge B, Zhang Y, Zhu H, Zhou H.
     

    Nomadic populations have played a significant role in the history of not only China but also in many nations worldwide. Because they had no written language, an important aspect in the study of these people is the discovery of their tombs. It has been generally accepted that Xiongnu was the first empire created by a nomadic tribe in the 3rd century BC. However, little population genetic information is available concerning the Donghu, another flourishing nomadic tribe at the same period because of the restriction of materials until the Jinggouzi site was excavated. In order to test the genetic characteristics of ancient people in this site and to explore the relationship between Jinggouzis and Donghus, two uniparentally inherited markers were analyzed from 42 human remains in this site, which was located in northern China, dated approximately 2500 years ago. With ancient DNA technology, four mtDNA haplogroups (D, G, C, and M10) and one Y chromosome haplogroup (C) were identified using mitochondrial DNA and Y-chromosome single nucleotide polymorphisms. Those haplogroups are common in North Asia and East Asia. The Jinggouzi people were genetically closest to the Xianbeis in ancient populations and to the Oroqens among extant populations, who were all pastoralists. This might indicate that ancient Jinggouzi people were nomads. Meanwhile, according to the genetic data and the evidences in archaeology, we inferred that Jinggouzi people were associated with Donghu. It is of much value to trace the history of the Donghu tribe and this might show some insight into the ancient nomadic society.

    Uniparental markers of contemporary Italian population reveals details on its pre-Roman heritage.
    Brisighelli F, Álvarez-Iglesias V, Fondevila M, Blanco-Verea A, Carracedo A, Pascali VL, Capelli C, Salas A. [FULL PAPER]
     

    BACKGROUND:
    According to archaeological records and historical documentation, Italy has been a melting point for populations of different geographical and ethnic matrices. Although Italy has been a favorite subject for numerous population genetic studies, genetic patterns have never been analyzed comprehensively, including uniparental and autosomal markers throughout the country.
    METHODS/PRINCIPAL FINDINGS:
    A total of 583 individuals were sampled from across the Italian Peninsula, from ten distant (if homogeneous by language) ethnic communities--and from two linguistic isolates (Ladins, Grecani Salentini). All samples were first typed for the mitochondrial DNA (mtDNA) control region and selected coding region SNPs (mtSNPs). This data was pooled for analysis with 3,778 mtDNA control-region profiles collected from the literature. Secondly, a set of Y-chromosome SNPs and STRs were also analyzed in 479 individuals together with a panel of autosomal ancestry informative markers (AIMs) from 441 samples. The resulting genetic record reveals clines of genetic frequencies laid according to the latitude slant along continental Italy--probably generated by demographical events dating back to the Neolithic. The Ladins showed distinctive, if more recent structure. The Neolithic contribution was estimated for the Y-chromosome as 14.5% and for mtDNA as 10.5%. Y-chromosome data showed larger differentiation between North, Center and South than mtDNA. AIMs detected a minor sub-Saharan component; this is however higher than for other European non-Mediterranean populations. The same signal of sub-Saharan heritage was also evident in uniparental markers.
    CONCLUSIONS/SIGNIFICANCE:
    Italy shows patterns of molecular variation mirroring other European countries, although some heterogeneity exists based on different analysis and molecular markers. From North to South, Italy shows clinal patterns that were most likely modulated during Neolithic times.

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    Qiaomei Fu et al., A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes, Current Biology, 21 March 2013.

    Recent analyses of de novo DNA mutations in modern humans have suggested a nuclear substitution rate that is approximately half that of previous estimates based on fossil calibration. This result has led to suggestions that major events in human evolution occurred far earlier than previously thought.

    Here, we use mitochondrial genome sequences from ten securely dated ancient modern humans spanning 40,000 years as calibration points for the mitochondrial clock, thus yielding a direct estimate of the mitochondrial substitution rate. Our clock yields mitochondrial divergence times that are in agreement with earlier estimates based on calibration points derived from either fossils or archaeological material. In particular, our results imply a separation of non-Africans from the most closely related sub-Saharan African mitochondrial DNAs (haplogroup L3) that occurred less than 62–95 kya.

    Though single loci like mitochondrial DNA (mtDNA) can only provide biased estimates of population divergence times, they can provide valid upper bounds. Our results exclude most of the older dates for African and non-African population divergences recently suggested by de novo mutation rate estimates in the nuclear genome.
    Coverage here: 'Out of Africa' Story Being Rewritten Again

    Our early human ancestors may have left Africa more recently than thought, between 62,000 and 95,000 years ago, suggests a new analysis of genetic material from fossil skeletons. The new findings are in line with earlier estimates, but contradict a more recent study that put humans' first exodus from Africa least 200,000 years ago. The new results "agree with what we know from archaeology," said study co-author Alissa Mittnik, a biologist at University of Tübingen, in Germany.
    Last edited by Jean M; 03-22-2013 at 12:29 AM.

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    Can't wait to see the paper - this group is doing some really great work. Some fascinating excerpts from the paper are quoted at ForumBiodiveristy.
    Here we use the complete or nearly complete mitochondrial genomes from ten ancient modern humans for which reliable radiocarbon dates are available to calculate the human mtDNA substitution rate directly. This strategy circumvents the limitations imposed by the use of indirect measures of substitution rates such as those obtained via fossil calibration. The samples used in this analysis span 40,000 years of human history and originate from Europe and Eastern Asia. We use our substitution rate to estimate the dates of major human evolutionary events in the last 200,000 years.
    All but one of the ancient modern human sequences from Europe belonged to mtDNA hg U, thus confirming previous findings that hg U was the dominant type of mtDNA before the spread of agriculture into Europe [15]. The exception was the Cro-Magnon 1 sample, which belonged to the derived hg T2b1, an unexpected hg given its putative age of 30,000 years [16]. Since the radiocarbon date for this specimen was obtained from an associated shell [16], we dated the sample itself using accelerator mass spectrometry (AMS). Surprisingly, the sample had a much younger age of about 700 years, suggesting a medieval origin. Consequently, this bone fragment has now been removed from the Cro-Magnon collection at the Musée de l’Homme in Paris.
    Using the substitution rate for the whole mtDNA genome obtained by Bayesian estimation, we estimated the time of the MRCA for all modern humans at 157 kya (120–197 kya, 95% HPD) (Table 2). Our rate also implies a split of all non-African hgs from the closest widespread sub-Saharan African hg (L3) of 78.3 kya (62.4–94.9 kya) (Table 3). The MRCA of hg Q, often referred to as a maximum age for the settlement of Australia, was calculated at 42 kya (30–54.9 kya) (Table 3). The time to most recent common ancestor (TMRCA) of hg U5, often argued to have evolved within the first early modern humans in Europe [18], was calculated at 29.6 kya (22.7–37.2 kya) (Table 3).
    The age estimate for U5 is nearly identical to the estimate from Behar et al 2012 of 30,248 +/- 5330. So it will be interesting to see the details.

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    Awesome stuff!

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    Meryanne K Tumonggor et al., The Indonesian archipelago: an ancient genetic highway linking Asia and the Pacific, Journal of Human Genetics (2013) 58, 165–173

    Indonesia, an island nation linking mainland Asia with the Pacific world, hosts a wide range of linguistic, ethnic and genetic diversity. Despite the complexity of this cultural environment, genetic studies in Indonesia remain surprisingly sparse. Here, we report mitochondrial DNA (mtDNA) and associated Y-chromosome diversity for the largest cohort of Indonesians examined to date—2740 individuals from 70 communities spanning 12 islands across the breadth of the Indonesian archipelago. We reconstruct 50 000 years of population movements, from mitochondrial lineages reflecting the very earliest settlers in island southeast Asia, to Neolithic population dispersals. Historic contacts from Chinese, Indians, Arabs and Europeans comprise a noticeable fraction of Y-chromosome variation, but are not reflected in the maternally inherited mtDNA. While this historic immigration favored men, patterns of genetic diversity show that women moved more widely in earlier times. However, measures of population differentiation signal that Indonesian communities are trending away from the matri- or ambilocality of early Austronesian societies toward the more common practice of patrilocal residence today. Such sex-specific dispersal patterns remain even after correcting for the different mutation rates of mtDNA and the Y chromosome. This detailed palimpsest of Indonesian genetic diversity is a direct outcome of the region’s complex history of immigration, transitory migrants and populations that have endured in situ since the region’s first settlement.

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    Reconstructing Roma History from Genome-Wide Data

    [Link]

    The Roma people, living throughout Europe and West Asia, are a diverse population linked by the Romani language and culture. Previous linguistic and genetic studies have suggested that the Roma migrated into Europe from South Asia about 1,000–1,500 years ago. Genetic inferences about Roma history have mostly focused on the Y chromosome and mitochondrial DNA. To explore what additional information can be learned from genome-wide data, we analyzed data from six Roma groups that we genotyped at hundreds of thousands of single nucleotide polymorphisms (SNPs). We estimate that the Roma harbor about 80% West Eurasian ancestry–derived from a combination of European and South Asian sources–and that the date of admixture of South Asian and European ancestry was about 850 years before present. We provide evidence for Eastern Europe being a major source of European ancestry, and North-west India being a major source of the South Asian ancestry in the Roma. By computing allele sharing as a measure of linkage disequilibrium, we estimate that the migration of Roma out of the Indian subcontinent was accompanied by a severe founder event, which appears to have been followed by a major demographic expansion after the arrival in Europe.
    Only immediate criticism of this paper is the complete absence of Middle-Eastern references in their comparisons. The Roma did pass through the Middle-East towards Europe and probably received some admixture along the way. I was informed there were Romani living in the Middle-East still, but after looking into the matter, it seems these people (Dom) are a seperate ethno-linguistic group, although I may be mistaken on this.

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    New British Isles paper

    A paper in the making rather than existing, but I thought this a good a place as any to post about this.

    http://www.justgiving.com/DNAforum

    Clicking 'Read more of my story' reveals some pretty juicy details regarding progress under DF49.

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    Peter Ralph and Graham Coop, The Geography of Recent Genetic Ancestry across Europe, PLoS Biology, vol. 11, no. 5 (May 2013), e1001555.

    This interesting paper was made available online in July last year prior to publication, and there was comment then in the blogosphere and forums, but it has gone through several revisions since then, and is worth a second look.)

    The recent genealogical history of human populations is a complex mosaic formed by individual migration, large-scale population movements, and other demographic events. Population genomics datasets can provide a window into this recent history, as rare traces of recent shared genetic ancestry are detectable due to long segments of shared genomic material. We make use of genomic data for 2,257 Europeans (in the Population Reference Sample [POPRES] dataset) to conduct one of the first surveys of recent genealogical ancestry over the past 3,000 years at a continental scale. We detected 1.9 million shared long genomic segments, and used the lengths of these to infer the distribution of shared ancestors across time and geography. We find that a pair of modern Europeans living in neighboring populations share around 2–12 genetic common ancestors from the last 1,500 years, and upwards of 100 genetic ancestors from the previous 1,000 years. These numbers drop off exponentially with geographic distance, but since these genetic ancestors are a tiny fraction of common genealogical ancestors, individuals from opposite ends of Europe are still expected to share millions of common genealogical ancestors over the last 1,000 years. There is also substantial regional variation in the number of shared genetic ancestors. For example, there are especially high numbers of common ancestors shared between many eastern populations that date roughly to the migration period (which includes the Slavic and Hunnic expansions into that region). Some of the lowest levels of common ancestry are seen in the Italian and Iberian peninsulas, which may indicate different effects of historical population expansions in these areas and/or more stably structured populations. Population genomic datasets have considerable power to uncover recent demographic history, and will allow a much fuller picture of the close genealogical kinship of individuals across the world.
    RalphCoop2013.jpg

    In the same issue Robin Meadows gives a quick and readable outline of this paper: Genomics Recapitulates History in Europe

    As might be expected, comparison of these long shared segments by country typically showed that recent relatedness is highest amongst people who live near each other. There are, however, some noteworthy departures from this norm. People in the UK share more recent ancestors with people in Ireland than with others living in their own country. Likewise, people in Germany share more recent ancestors with the Polish than with other Germans. This pattern could reflect the migrations of smaller populations into a larger one.

    Similarly, while recent relatedness generally drops evenly across geographic distances in Europe, a few exceptions stand out. Regardless of physical proximity, recent relatedness is low between the Italian peninsula and the rest of the continent. At the other end of the scale, recent relatedness is high within northern Europe as well as across eastern Europe – three times that within other regions at similar distances...

    Another intriguing finding is that the numbers and timing of common ancestors among different parts of Europe may reflect major events in the continent's history. Notably, the number of common ancestors within the last 1,000 to 2,000 years is particularly high within eastern Europe — similar to those in Ireland despite spanning far greater distances — and the timing fits with the series of migrations that began with the Huns in the 4th century and ended with the Slavs between the 6th and 10th centuries.

    In support of linking this spike in common ancestry with these migrations, many of today's eastern Europeans who share long segments also speak Slavic languages.
    Furthermore, the regions with the fewest common ancestors (France, and the Italian and Iberian peninsulas) are also thought to have been largely untouched by the migrations of Huns and Slavs.
    Last edited by Jean M; 05-08-2013 at 12:37 PM. Reason: Correcting typos.

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  17. #10
    The paper has been posted by David Faux on Rootsweb and it has done justice to me (like Gioiello, Maliclavelli etc.): the impact on Italian population of the Celtic invasion, of the Greek colonization, of the millions of slaves during the Roman Empire, of the Barbarian invasions (or, if you prefer, of the migrations of people or Voelkerwanderungen) etc. has been minimal, what I have always supported. About what happened before, we probably will know something more careful next.
    It remains the possibility that what came back to Italy and Iberia were those who had come out before.

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